Microscopy-based assessment of RNA polymerase II clusters during early stages of zebrafish embryo development
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This repository contains the data and MatLab analysis scripts of the analysis of RNA polymerase II clusters over the course of zygotic genome activation and gastrulation of zebrafish embryos. Samples were prepared and images were recorded by Irina Mamontova and Agnieszka Pancholi in Lennart Hilbert's laboratory, images were analyzed by Lennart Hilbert. To analyse date data, the raw image data are first extracted into MatLab-native files using the MultiPosition_extraction_nd2.m script. The actual analysis is then carried out using the ClusterAnalysis.m script. Example microscopy images were produced using the ExampleImages.m script. The extracted data can be reviewed using the ReviewExtractedStacks.m script. For the analysis of nuclear and Pol II cluster properties, the following script was used: ClusterAnalysis.m After the primary image analysis, the following MatLab workspace save file was created, which allows obtaining the final analysis results: StageFigure_IntermediateSave_28Sep2025.mat For the analysis of cluster volume and solidity over developmental stages, a different script with minimal cluster volume of 0.01 µm^3 was used: ClusterAnalysis_VolumeThreshold_0_01.m After the primary image analysis, the following MatLab workspace save file was created, which allows obtaining the final analysis results: ModelFigure_IntermediateSave_Vol0_01um_11Jan2026.matThe raw image data will be uploaded to additional Zenodo repositories, which will be linked here after completion of the uploads. The reserved DOIs are: 10.5281/zenodo.18436843 (Oblong, Sphere, Dome) https://doi.org/10.5281/zenodo.18436851 (30% Epiboly, 50% Epiboly) https://doi.org/10.5281/zenodo.18436843
本仓库包含针对斑马鱼胚胎合子基因组激活（zygotic genome activation）与原肠胚形成（gastrulation）过程中RNA聚合酶II（RNA polymerase II）簇开展分析的相关数据及MATLAB分析脚本。实验样本制备与图像采集由伦纳特·希贝尔（Lennart Hilbert）实验室的伊琳娜·马蒙托娃（Irina Mamontova）与阿格涅什卡·潘乔利（Agnieszka Pancholi）完成，图像分析由伦纳特·希贝尔执行。 若需处理图像数据，需首先通过MultiPosition_extraction_nd2.m脚本将原始图像数据转换为MATLAB原生格式文件。后续实际分析通过ClusterAnalysis.m脚本完成。示例显微图像由ExampleImages.m脚本生成。可通过ReviewExtractedStacks.m脚本对提取后的数据进行检视。 针对细胞核与Pol II簇属性的分析，采用如下脚本：ClusterAnalysis.m。 在初步图像分析完成后，将生成如下MATLAB工作区保存文件，可用于获取最终分析结果：StageFigure_IntermediateSave_28Sep2025.mat。 针对不同发育阶段的簇体积与密实度分析，则采用了将簇最小体积阈值设为0.01 µm³的另一脚本：ClusterAnalysis_VolumeThreshold_0_01.m。 在初步图像分析完成后，将生成如下MATLAB工作区保存文件，可用于获取最终分析结果：ModelFigure_IntermediateSave_Vol0_01um_11Jan2026.mat。 原始图像数据将上传至额外的Zenodo仓储，上传完成后将在此处附上相关链接。预留的数字对象标识符（DOI）如下： 1. 10.5281/zenodo.18436843（长圆形期、球形期、穹顶期） 2. https://doi.org/10.5281/zenodo.18436851（30%外包期、50%外包期） 3. https://doi.org/10.5281/zenodo.18436843
